A fine-scale Arabidopsis chromatin landscape reveals chromatin conformation-associated transcriptional dynamics

Yueying Zhang, Qianli Dong, Zhen Wang, Qinzhe Liu, Haopeng Yu, Wenqing Sun, Jitender Cheema, Qiancheng You, Ling Ding, Xiaofeng Cao, Chuan He, Yiliang Ding () and Huakun Zhang ()
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Yueying Zhang: Northeast Normal University
Qianli Dong: Northeast Normal University
Zhen Wang: John Innes Centre
Qinzhe Liu: The University of Chicago
Haopeng Yu: John Innes Centre
Wenqing Sun: Northeast Normal University
Jitender Cheema: John Innes Centre
Qiancheng You: The University of Chicago
Ling Ding: Northeast Normal University
Xiaofeng Cao: Chinese Academy of Sciences
Chuan He: The University of Chicago
Yiliang Ding: John Innes Centre
Huakun Zhang: Northeast Normal University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Plants, as sessile organisms, deploy transcriptional dynamics for adapting to extreme growth conditions such as cold stress. Emerging evidence suggests that chromatin architecture contributes to transcriptional regulation. However, the relationship between chromatin architectural dynamics and transcriptional reprogramming in response to cold stress remains unclear. Here, we apply a chemical-crosslinking assisted proximity capture (CAP-C) method to elucidate the fine-scale chromatin landscape, revealing chromatin interactions within gene bodies closely associated with RNA polymerase II (Pol II) densities across initiation, pausing, and termination sites. We observe dynamic changes in chromatin interactions alongside Pol II activity alterations during cold stress, suggesting local chromatin dynamics may regulate Pol II activity. Notably, cold stress does not affect large-scale chromatin conformations. We further identify a comprehensive promoter-promoter interaction (PPI) network across the genome, potentially facilitating co-regulation of gene expression in response to cold stress. Our study deepens the understanding of chromatin conformation-associated gene regulation in plant response to cold.

Date: 2024
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DOI: 10.1038/s41467-024-47678-7

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